Two violations of environmental law require further analysis of a massive wind farm planned for the Nantucket Sound, a federal judge ruled.

Plans for the Nantucket Sound wind farm have been a great controversy since Cape Wind LLC filed for project permits in 2001, pitting environmentalists against environmentalists in a green civil war.

Supporters herald the project’s clean energy potential while opponents – including a Native American tribe, boaters and fisherman – say the windmills will pollute the scenery and kill sea birds and whales.

Consolidated before U.S. District Judge Reggie Walton, the case includes four complaints that environmental groups, the Wampanoag Tribe of Gay Head and others brought against the federal agencies including the U.S. Bureau of Ocean Energy Management, the Department of the Interior, U.S. Fish and Wildlife Service, the National Marine Fisheries Service and the Army Corps of Engineers.

“The Cape Wind project has been described as ‘the first of its kind in the United States and is one of the largest offshore wind projects in the world,'” Walton explained.

Environmental groups like Public Employees for Environmental Responsibility accused the agencies of having violated the Endangered Species Act, the Migratory Bird Treaty Act and the National Environmental Policy Act in approving the project.

Meanwhile the town of Barnstable, Mass., alleged violations of the Outer Continental Shelf Lands Act, and the Wampanoag said that the threat to their religious freedom and their fish supply amounts to a violation of the National Historic Preservation Act.

In an 88-page navigation of the case Friday, Judge Walton granted the agencies summary judgment all but two claims.

One of those claims, which Walton instead decided for the plaintiffs, involves the roseate tern and piping plover, two birds listed under the Endangered Species Act (ESA) that the Cape Wind project could harm.

In sidelining concerns for the birds, Fish and Wildlife (FWS) considered, but ultimately did not pursue, a measure called the “feathering operational adjustment,” according to the ruling.

This adjustment would have required the temporary and seasonal shut down of the wind turbine generators through the feathering of the rotors.

Judge Walton called it “unacceptable” that FWS failed to make an independent determination before “casting away the feathering measure.”

“While it is certainly possible that the feathering measure would not comport with [federal law], the ESA and its implementing regulations require the FWS to make an independent determination,” he wrote. “Because it seemingly did not do so, the court must grant summary judgment to the plaintiffs on their ESA claims against the FWS.”

Walton also granted the plaintiffs summary judgment on their claims that the National Marine Fisheries Service violated the ESA by failing to issue an incidental take statement for the take of North Atlantic right whales.

The harassment, killing or otherwise harming of any threatened or endangered species are among several actions that qualifies as a take under the ESA.

“Here, the NMFS included no incidental take statement for right whales, despite the fact that the whales have traversed the Cape Wind project area and appeared along routes that will be traveled by project vessels,” Walton wrote. “And while the biological opinion states that the ‘NMFS [] concluded that the proposed action is not likely to adversely affect right … whales and, therefore, is not likely to jeopardize the[ir] continued existence,’ the NMFS did not state that incidental take would not occur or was ‘not anticipated.’ Accordingly, because incidental take ‘may occur,’ the NMFS was required to include an incidental take statement with its biological opinion, and its failure to do so was arbitrary and capricious.”

In siding with the government on all other claims, Walton found no showing that the government erred in its approval procedure.

The ruling notes that offshore sites around Portland, Maine; Block Island, R.I.; and Boston, Mass., were among those considered.

Cape Wind’s website says the wind farm will be the first offshore wind farm in the United States, producing more than 420 megawatts of power while reducing “global warming greenhouse gas emissions by 734,000 tons per year.”

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